setdircommand.cpp

   1 /*
   2  *  setoutdircommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 1/21/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "setdircommand.h"
  11
  12 //**********************************************************************************************************************
  13
  14 SetDirectoryCommand::SetDirectoryCommand(string option)  {
  15         try {
  16                 abort = false;
  17
  18                 //allow user to run help
  19                 if(option == "help") { help(); abort = true; }
  20
  21                 else {
  22                         //valid paramters for this command
  23                         string Array[] =  {"output","input","tempdefault","outputdir","inputdir"};
  24                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  25
  26                         OptionParser parser(option);
  27                         map<string, string> parameters = parser.getParameters();
  28
  29                         ValidParameters validParameter;
  30                         //check to make sure all parameters are valid for command
  31                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  32                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  33                         }
  34
  35                         output = validParameter.validFile(parameters, "output", false);
  36                         if (output == "not found") {  output = "";  }
  37
  38                         input = validParameter.validFile(parameters, "input", false);
  39                         if (input == "not found") {  input = "";  }
  40
  41                         tempdefault = validParameter.validFile(parameters, "tempdefault", false);
  42                         if (tempdefault == "not found") {  tempdefault = "";  }
  43
  44                         if ((input == "") && (output == "") && (tempdefault == "")) {
  45                                 m->mothurOut("You must provide either an input, output or tempdefault for the set.outdir command."); m->mothurOutEndLine(); abort = true;
  46                         }
  47                 }
  48         }
  49         catch(exception& e) {
  50                 m->errorOut(e, "SetDirectoryCommand", "SetDirectoryCommand");
  51                 exit(1);
  52         }
  53 }
  54 //**********************************************************************************************************************
  55
  56 void SetDirectoryCommand::help(){
  57         try {
  58                 m->mothurOut("The set.dir command can be used to direct the output files generated by mothur to a specific place, the directory must exist.\n");
  59                 m->mothurOut("The set.dir command can also be used to specify the directory where your input files are located, the directory must exist.\n");
  60                 m->mothurOut("The set.dir command can also be used to override or set the default location mothur will look for files if it is unable to find them, the directory must exist.\n");
  61                 m->mothurOut("The set.dir command parameters are input, output and tempdefault and one is required.\n");
  62                 m->mothurOut("To return the output to the same directory as the input files you may enter: output=clear.\n");
  63                 m->mothurOut("To return the input to the current working directory you may enter: input=clear.\n");
  64                 m->mothurOut("To set the output to the directory where mothur.exe is located you may enter: output=default.\n");
  65                 m->mothurOut("To set the input to the directory where mothur.exe is located you may enter: input=default.\n");
  66                 m->mothurOut("To return the tempdefault to the default you provided at compile time you may enter: tempdefault=clear.\n");
  67                 m->mothurOut("To set the tempdefault to the directory where mothur.exe is located you may enter: tempdefault=default.\n");
  68                 m->mothurOut("The set.dir command should be in the following format: set.dir(output=yourOutputDirectory, input=yourInputDirectory, tempdefault=yourTempDefault).\n");
  69                 m->mothurOut("Example set.outdir(output=/Users/lab/desktop/outputs, input=/Users/lab/desktop/inputs).\n");
  70                 m->mothurOut("Note: No spaces between parameter labels (i.e. output), '=' and parameters (i.e.yourOutputDirectory).\n\n");
  71         }
  72         catch(exception& e) {
  73                 m->errorOut(e, "SetDirectoryCommand", "help");
  74                 exit(1);
  75         }
  76 }
  77 //**********************************************************************************************************************
  78
  79 SetDirectoryCommand::~SetDirectoryCommand(){}
  80
  81 //**********************************************************************************************************************
  82
  83 int SetDirectoryCommand::execute(){
  84         try {
  85
  86                 if (abort == true) { return 0; }
  87
  88                 commandFactory = CommandFactory::getInstance();
  89
  90                 //redirect output
  91                 if ((output == "clear") || (output == "")) {  output = "";  commandFactory->setOutputDirectory(output);  }
  92                 else if (output == "default") {
  93                         GlobalData* globaldata = GlobalData::getInstance();
  94                         string exepath = globaldata->argv;
  95                         output = exepath.substr(0, (exepath.find_last_of('m')));
  96
  97                         m->mothurOut("Changing output directory to " + output); m->mothurOutEndLine();
  98                         commandFactory->setOutputDirectory(output);
  99                 }else {
 100                         //add / to name if needed
 101                         string lastChar = output.substr(output.length()-1);
 102                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 103                                 if (lastChar != "/") { output += "/"; }
 104                         #else
 105                                 if (lastChar != "\\") { output += "\\"; }
 106                         #endif
 107
 108                         //test to make sure directory exists
 109                         output = m->getFullPathName(output);
 110                         string outTemp = output + "temp";
 111                         ofstream out;
 112                         out.open(outTemp.c_str(), ios::trunc);
 113                         if(!out) {
 114                                 m->mothurOut(output + " directory does not exist or is not writable."); m->mothurOutEndLine();
 115                         }else{
 116                                 out.close();
 117                                 remove(outTemp.c_str());
 118                                 m->mothurOut("Changing output directory to " + output); m->mothurOutEndLine();
 119                                 commandFactory->setOutputDirectory(output);
 120                         }
 121                 }
 122
 123                 //redirect input
 124                 if ((input == "clear") || (input == "")) {  input = "";  commandFactory->setInputDirectory(input);  }
 125                 else if (input == "default") {
 126                         GlobalData* globaldata = GlobalData::getInstance();
 127                         string exepath = globaldata->argv;
 128                         input = exepath.substr(0, (exepath.find_last_of('m')));
 129
 130                         m->mothurOut("Changing input directory to " + input); m->mothurOutEndLine();
 131                         commandFactory->setInputDirectory(input);
 132                 }else {
 133                         //add / to name if needed
 134                         string lastChar = input.substr(input.length()-1);
 135                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 136                                 if (lastChar != "/") { input += "/"; }
 137                         #else
 138                                 if (lastChar != "\\") { input += "\\"; }
 139                         #endif
 140
 141                         //test to make sure directory exists
 142                         input = m->getFullPathName(input);
 143                         string inTemp = input + "temp";
 144                         ofstream in;
 145                         in.open(inTemp.c_str(), ios::trunc);
 146                         if(!in) {
 147                                 m->mothurOut(input + " directory does not exist or is not writable."); m->mothurOutEndLine();
 148                         }else{
 149                                 in.close();
 150                                 remove(inTemp.c_str());
 151                                 m->mothurOut("Changing input directory to " + input); m->mothurOutEndLine();
 152                                 commandFactory->setInputDirectory(input);
 153                         }
 154                 }
 155
 156                 //set default
 157                 if (tempdefault == "clear") {
 158                         #ifdef MOTHUR_FILES
 159                                 string temp = MOTHUR_FILES;
 160                                 m->mothurOut("Resetting default directory to " + temp); m->mothurOutEndLine();
 161                                 m->setDefaultPath(temp);
 162                         #else
 163                                 string temp = "";
 164                                 m->mothurOut("No default directory defined at compile time."); m->mothurOutEndLine();
 165                                 m->setDefaultPath(temp);
 166                         #endif
 167                 }else if (tempdefault == "") {  //do nothing
 168                 }else if (tempdefault == "default") {
 169                         GlobalData* globaldata = GlobalData::getInstance();
 170                         string exepath = globaldata->argv;
 171                         tempdefault = exepath.substr(0, (exepath.find_last_of('m')));
 172
 173                         m->mothurOut("Changing default directory to " + tempdefault); m->mothurOutEndLine();
 174                         m->setDefaultPath(tempdefault);
 175                 }else {
 176                         //add / to name if needed
 177                         string lastChar = tempdefault.substr(tempdefault.length()-1);
 178                         #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
 179                                 if (lastChar != "/") { tempdefault += "/"; }
 180                         #else
 181                                 if (lastChar != "\\") { tempdefault += "\\"; }
 182                         #endif
 183
 184                         m->mothurOut("Changing default directory to " + tempdefault); m->mothurOutEndLine();
 185                         m->setDefaultPath(tempdefault);
 186                 }
 187
 188                 return 0;
 189         }
 190         catch(exception& e) {
 191                 m->errorOut(e, "SetDirectoryCommand", "execute");
 192                 exit(1);
 193         }
 194 }
 195 //**********************************************************************************************************************/